############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r methylPipe -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data methylPipe ### ############################################################################## ############################################################################## * checking for file 'methylPipe/DESCRIPTION' ... OK * preparing 'methylPipe': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'methylPipe.rnw' using knitr Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'methylPipe' Loading required package: BSgenome Loading required package: rtracklayer Extracting methylation information from input SAM files and creating output files for each sample... Creating temporary BAM files from input SAM files... Creating uncovered regions objects for each sample from BAM files... Removing all temporary BAM files... Methylation info and Uncovered regions output files created for each sample in output_folder... Processing done Successfully... Warning in in_dir(input_dir(), expr) : You changed the working directory to C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmpy8IjKc (probably via setwd()). It will be restored to C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpEPbWHS/Rbuildf2074c8b80/methylPipe/vignettes. See the Note section in ?knitr::knit S4 Object of class BSdata TABIX indexed file for this BSdata: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpEPbWHS/Rinstf2059c74ec3/methylPipe/extdata/H1_chr20_CG_10k_tabix_out.txt.gz The first lines of the uncovered regions of this BSdata: Associated organism genome: Homo sapiens Chromosomes available: The first lines of the data: Quitting from lines 170-174 (methylPipe.rnw) Error: processing vignette 'methylPipe.rnw' failed with diagnostics: could not find function "clusterApplyLB" --- failed re-building 'methylPipe.rnw' Warning in file.remove(f) : cannot remove file 'clusterlog.txt', reason 'Permission denied' SUMMARY: processing the following file failed: 'methylPipe.rnw' Error: Vignette re-building failed. Execution halted